<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "https://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
<meta http-equiv="X-UA-Compatible" content="IE=9"/>
<meta name="generator" content="Doxygen 1.8.16"/>
<meta name="viewport" content="width=device-width, initial-scale=1"/>
<title>ClaraGenomicsAnalysis: common/utils/include/claragenomics/utils/genomeutils.hpp Source File</title>
<link href="tabs.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="jquery.js"></script>
<script type="text/javascript" src="dynsections.js"></script>
<link href="search/search.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="search/searchdata.js"></script>
<script type="text/javascript" src="search/search.js"></script>
<link href="doxygen.css" rel="stylesheet" type="text/css" />
</head>
<body>
<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
<div id="titlearea">
<table cellspacing="0" cellpadding="0">
 <tbody>
 <tr style="height: 56px;">
  <td id="projectalign" style="padding-left: 0.5em;">
   <div id="projectname">ClaraGenomicsAnalysis
   &#160;<span id="projectnumber">0.4.0</span>
   </div>
  </td>
 </tr>
 </tbody>
</table>
</div>
<!-- end header part -->
<!-- Generated by Doxygen 1.8.16 -->
<script type="text/javascript">
/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&amp;dn=gpl-2.0.txt GPL-v2 */
var searchBox = new SearchBox("searchBox", "search",false,'Search');
/* @license-end */
</script>
<script type="text/javascript" src="menudata.js"></script>
<script type="text/javascript" src="menu.js"></script>
<script type="text/javascript">
/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&amp;dn=gpl-2.0.txt GPL-v2 */
$(function() {
  initMenu('',true,false,'search.php','Search');
  $(document).ready(function() { init_search(); });
});
/* @license-end */</script>
<div id="main-nav"></div>
<!-- window showing the filter options -->
<div id="MSearchSelectWindow"
     onmouseover="return searchBox.OnSearchSelectShow()"
     onmouseout="return searchBox.OnSearchSelectHide()"
     onkeydown="return searchBox.OnSearchSelectKey(event)">
</div>

<!-- iframe showing the search results (closed by default) -->
<div id="MSearchResultsWindow">
<iframe src="javascript:void(0)" frameborder="0" 
        name="MSearchResults" id="MSearchResults">
</iframe>
</div>

<div id="nav-path" class="navpath">
  <ul>
<li class="navelem"><a class="el" href="dir_bdd9a5d540de89e9fe90efdfc6973a4f.html">common</a></li><li class="navelem"><a class="el" href="dir_85effdddc426fd82e3610be0948fd413.html">utils</a></li><li class="navelem"><a class="el" href="dir_cbd0fd5fcc23422502de88d4fe6e7386.html">include</a></li><li class="navelem"><a class="el" href="dir_8e216217187728c84aa14a4942da12a2.html">claragenomics</a></li><li class="navelem"><a class="el" href="dir_657c9b9511f57ce884717ee8b069b43d.html">utils</a></li>  </ul>
</div>
</div><!-- top -->
<div class="header">
  <div class="headertitle">
<div class="title">genomeutils.hpp</div>  </div>
</div><!--header-->
<div class="contents">
<div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="comment">/*</span></div>
<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">* Copyright (c) 2019, NVIDIA CORPORATION.  All rights reserved.</span></div>
<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">*</span></div>
<div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="comment">* NVIDIA CORPORATION and its licensors retain all intellectual property</span></div>
<div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="comment">* and proprietary rights in and to this software, related documentation</span></div>
<div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<span class="comment">* and any modifications thereto.  Any use, reproduction, disclosure or</span></div>
<div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="comment">* distribution of this software and related documentation without an express</span></div>
<div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<span class="comment">* license agreement from NVIDIA CORPORATION is strictly prohibited.</span></div>
<div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;<span class="comment">*/</span></div>
<div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160; </div>
<div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;<span class="preprocessor">#pragma once</span></div>
<div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160; </div>
<div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;<span class="preprocessor">#include &lt;random&gt;</span></div>
<div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160;<span class="preprocessor">#include &lt;stdexcept&gt;</span></div>
<div class="line"><a name="l00015"></a><span class="lineno">   15</span>&#160; </div>
<div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160;<span class="keyword">namespace </span>claragenomics</div>
<div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;{</div>
<div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160; </div>
<div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;<span class="keyword">namespace </span>genomeutils</div>
<div class="line"><a name="l00020"></a><span class="lineno">   20</span>&#160;{</div>
<div class="line"><a name="l00021"></a><span class="lineno">   21</span>&#160; </div>
<div class="line"><a name="l00022"></a><span class="lineno">   22</span>&#160;<span class="keyword">inline</span> std::string generate_random_genome(<span class="keyword">const</span> int32_t length, std::minstd_rand&amp; rng)</div>
<div class="line"><a name="l00023"></a><span class="lineno">   23</span>&#160;{</div>
<div class="line"><a name="l00024"></a><span class="lineno">   24</span>&#160;    <span class="keyword">const</span> <span class="keywordtype">char</span> alphabet[4] = {<span class="charliteral">&#39;A&#39;</span>, <span class="charliteral">&#39;C&#39;</span>, <span class="charliteral">&#39;G&#39;</span>, <span class="charliteral">&#39;T&#39;</span>};</div>
<div class="line"><a name="l00025"></a><span class="lineno">   25</span>&#160;    std::uniform_int_distribution&lt;int32_t&gt; random_index(0, 3);</div>
<div class="line"><a name="l00026"></a><span class="lineno">   26</span>&#160;    std::string genome = <span class="stringliteral">&quot;&quot;</span>;</div>
<div class="line"><a name="l00027"></a><span class="lineno">   27</span>&#160;    <span class="keywordflow">for</span> (int32_t i = 0; i &lt; length; i++)</div>
<div class="line"><a name="l00028"></a><span class="lineno">   28</span>&#160;    {</div>
<div class="line"><a name="l00029"></a><span class="lineno">   29</span>&#160;        genome += alphabet[random_index(rng)];</div>
<div class="line"><a name="l00030"></a><span class="lineno">   30</span>&#160;    }</div>
<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;    <span class="keywordflow">return</span> genome;</div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;}</div>
<div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160; </div>
<div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;<span class="keyword">inline</span> std::vector&lt;std::string&gt; generate_random_sequences(std::string backbone,</div>
<div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;                                                          <span class="keywordtype">int</span> n,</div>
<div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;                                                          std::minstd_rand&amp; rng,</div>
<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;                                                          <span class="keywordtype">int</span> num_mutations = 1,</div>
<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;                                                          <span class="keywordtype">int</span> num_insertion = 1,</div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;                                                          <span class="keywordtype">int</span> num_deletions = 1)</div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;{</div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;    <span class="keywordflow">if</span> (backbone.length() == 0)</div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;        <span class="keywordflow">throw</span> std::invalid_argument(<span class="stringliteral">&quot;backbone sequence shouldn&#39;t be empty.&quot;</span>);</div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;    <span class="keywordflow">if</span> (backbone.length() &lt; num_deletions)</div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;        <span class="keywordflow">throw</span> std::invalid_argument(<span class="stringliteral">&quot;num_deletions should be smaller than backbone&#39;s length.&quot;</span>);</div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160; </div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;    std::vector&lt;std::string&gt; sequences(n, backbone);</div>
<div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;    std::string bases = <span class="stringliteral">&quot;ATCG&quot;</span>;</div>
<div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160; </div>
<div class="line"><a name="l00049"></a><span class="lineno">   49</span>&#160;    std::uniform_real_distribution&lt;double&gt; random_prob(0, 1);</div>
<div class="line"><a name="l00050"></a><span class="lineno">   50</span>&#160;    std::uniform_int_distribution&lt;int&gt; random_base_pos(0, bases.length() - 1);</div>
<div class="line"><a name="l00051"></a><span class="lineno">   51</span>&#160; </div>
<div class="line"><a name="l00052"></a><span class="lineno">   52</span>&#160;    <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 1; i &lt; n; i++)</div>
<div class="line"><a name="l00053"></a><span class="lineno">   53</span>&#160;    {</div>
<div class="line"><a name="l00054"></a><span class="lineno">   54</span>&#160;        <span class="keywordflow">for</span> (<span class="keywordtype">int</span> j = 0; j &lt; num_deletions; j++)</div>
<div class="line"><a name="l00055"></a><span class="lineno">   55</span>&#160;        {</div>
<div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160;            <span class="keywordflow">if</span> (random_prob(rng) &gt; 0.5)</div>
<div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160;            {</div>
<div class="line"><a name="l00058"></a><span class="lineno">   58</span>&#160;                <span class="keywordtype">int</span> length = sequences[i].length();</div>
<div class="line"><a name="l00059"></a><span class="lineno">   59</span>&#160;                std::uniform_int_distribution&lt;int&gt; random_del_pos(0, length - 1);</div>
<div class="line"><a name="l00060"></a><span class="lineno">   60</span>&#160;                <span class="keywordtype">int</span> del_pos = random_del_pos(rng);</div>
<div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;                sequences[i].erase(del_pos, 1);</div>
<div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160;            }</div>
<div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;        }</div>
<div class="line"><a name="l00064"></a><span class="lineno">   64</span>&#160; </div>
<div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;        <span class="keywordflow">for</span> (<span class="keywordtype">int</span> j = 0; j &lt; num_insertion; j++)</div>
<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;        {</div>
<div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;            <span class="keywordflow">if</span> (random_prob(rng) &gt; 0.5)</div>
<div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;            {</div>
<div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;                <span class="keywordtype">int</span> length = sequences[i].length();</div>
<div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;                std::uniform_int_distribution&lt;int&gt; random_ins_pos(0, length - 1);</div>
<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;                <span class="keywordtype">int</span> ins_pos  = random_ins_pos(rng);</div>
<div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;                <span class="keywordtype">int</span> ins_base = random_base_pos(rng);</div>
<div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160; </div>
<div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;                sequences[i].insert(ins_pos, 1, bases[ins_base]);</div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;            }</div>
<div class="line"><a name="l00076"></a><span class="lineno">   76</span>&#160;        }</div>
<div class="line"><a name="l00077"></a><span class="lineno">   77</span>&#160; </div>
<div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160;        <span class="keywordtype">int</span> length = sequences[i].length();</div>
<div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;        std::uniform_int_distribution&lt;int&gt; random_mut_pos(0, length - 1);</div>
<div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;        <span class="keywordflow">for</span> (<span class="keywordtype">int</span> j = 0; j &lt; num_mutations; j++)</div>
<div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;        {</div>
<div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;            <span class="keywordflow">if</span> (random_prob(rng) &gt; 0.5)</div>
<div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;            {</div>
<div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;                <span class="keywordtype">int</span> mut_pos           = random_mut_pos(rng);</div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;                <span class="keywordtype">int</span> swap_base         = random_base_pos(rng);</div>
<div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;                sequences[i][mut_pos] = bases[swap_base];</div>
<div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160;            }</div>
<div class="line"><a name="l00088"></a><span class="lineno">   88</span>&#160;        }</div>
<div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;    }</div>
<div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160; </div>
<div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;    <span class="keywordflow">return</span> sequences;</div>
<div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;}</div>
<div class="line"><a name="l00093"></a><span class="lineno">   93</span>&#160; </div>
<div class="line"><a name="l00094"></a><span class="lineno">   94</span>&#160;} <span class="comment">// namespace genomeutils</span></div>
<div class="line"><a name="l00095"></a><span class="lineno">   95</span>&#160; </div>
<div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;} <span class="comment">// namespace claragenomics</span></div>
</div><!-- fragment --></div><!-- contents -->
<!-- start footer part -->
<hr class="footer"/><address class="footer"><small>
Generated by &#160;<a href="http://www.doxygen.org/index.html">
<img class="footer" src="doxygen.png" alt="doxygen"/>
</a> 1.8.16
</small></address>
</body>
</html>
